The human oral microbiome has primarily been studied in clinical settings and for medical purposes. More recently, oral microbial research has been incorporated into other areas of study. In forensics, research has aimed to exploit the variation in composition of the oral microbiome to answer forensic relevant topics, such as human identification and geographical provenience. Several studies have focused on the use of microbiome for continental, national, or ethnic origin evaluations. However, it is not clear how the microbiome varies between similar ethnic populations across different regions in a country. We report here a comparison of the oral microbiomes of individuals living in two regions of Italy – Lombardy and Piedmont. Oral samples were obtained by swabbing the donors’ oral mucosa, and the V4 region of the 16S rRNA gene was sequenced from the extracted microbial DNA. Additionally, we compared the oral and the skin microbiome from a subset of these individuals, to provide an understanding of which anatomical region may provide more robust results that can be useful for forensic human identification. Initial analysis of the oral microbiota revealed the presence of a core oral microbiome, consisting of nine taxa shared across all oral samples, as well as unique donor characterising taxa in 31 out of 50 samples. We also identified a trend between the abundance of Proteobacteria and Bacteroidota and the smoking habits, and of Spirochaetota and Synergistota and the age of the enrolled participants. Whilst no significant differences were observed in the oral microbial diversity of individuals from Lombardy or Piedmont, we identified two bacterial families – Corynebacteriaceae and Actinomycetaceae – that showed abundance trends between the two regions. Comparative analysis of the skin and oral microbiota showed significant differences in the alpha (p = 0.0011) and beta (Pr(>F) = 9.999e-05) diversities. Analysis of skin and oral samples from the same donor further revealed that the skin microbiome contained more unique donor characterising taxa than the oral one. Overall, this study demonstrates that whilst the oral microbiome of individuals from the same country and of similar ethnicity are largely similar, there may be donor characterising taxa that might be useful for identification purposes. Furthermore, the bacterial signatures associated with certain lifestyles could provide useful information for investigative purposes. Finally, additional studies are required, the skin microbiome may be a better discriminant for human identification than the oral one.